Code
if(base::interactive()) {
params <- rmarkdown::yaml_front_matter(here::here("analysis/03_beta_diversity.qmd"))$params
}
factor_of_interest <- params$factor_of_interestSee the documentation of the MiscMetabar package for example of alpha diversity analysis.
Code
library(knitr)
library(targets)
library(MiscMetabar)
here::i_am("analysis/02_alpha_diversity.qmd")
source(here::here("R/styles.R"))Code
d_pq <- clean_pq(tar_read("d_vs", store=here::here("_targets/")))Cleaning suppress 2 taxa and 12 samples.Code
hill_pq(d_pq, factor_of_interest, one_plot = TRUE) &
(
theme_idest(
subtitle_size = 8,
plot_title_size = 12,
plot_margin = margin(5, 10, 5, 10),
axis_title_size = 9,
axis_text_size = 8
) + theme(legend.position = "none")
) Taxa are now in rows.
Code
ggbetween_pq(d_pq, factor_of_interest)$plot_Hill_0
$plot_Hill_1
$plot_Hill_2
Session Information
Session information are detailed below. More information about the machine, the system, as well as python and R packages, are available in the file data/data_final/information_run.txt .
Code
sessionInfo()R version 4.4.2 (2024-10-31)
Platform: x86_64-pc-linux-gnu
Running under: Debian GNU/Linux 12 (bookworm)
Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.11.0
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.11.0
locale:
[1] LC_CTYPE=fr_FR.UTF-8 LC_NUMERIC=C
[3] LC_TIME=fr_FR.UTF-8 LC_COLLATE=fr_FR.UTF-8
[5] LC_MONETARY=fr_FR.UTF-8 LC_MESSAGES=fr_FR.UTF-8
[7] LC_PAPER=fr_FR.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=fr_FR.UTF-8 LC_IDENTIFICATION=C
time zone: Europe/Paris
tzcode source: system (glibc)
attached base packages:
[1] stats graphics grDevices datasets utils methods base
other attached packages:
[1] MiscMetabar_0.10.1 purrr_1.0.2 dplyr_1.1.4 dada2_1.34.0
[5] Rcpp_1.0.13-1 ggplot2_3.5.1 phyloseq_1.50.0 targets_1.9.0
[9] knitr_1.49
loaded via a namespace (and not attached):
[1] RColorBrewer_1.1-3 rstudioapi_0.17.1
[3] jsonlite_1.8.9 datawizard_0.13.0
[5] correlation_0.8.6 magrittr_2.0.3
[7] SuppDists_1.1-9.8 farver_2.1.2
[9] rmarkdown_2.29 zlibbioc_1.52.0
[11] vctrs_0.6.5 multtest_2.62.0
[13] memoise_2.0.1 Rsamtools_2.22.0
[15] paletteer_1.6.0 effectsize_0.8.9
[17] htmltools_0.5.8.1 S4Arrays_1.6.0
[19] BWStest_0.2.3 Rhdf5lib_1.28.0
[21] SparseArray_1.6.0 rhdf5_2.50.0
[23] htmlwidgets_1.6.4 plyr_1.8.9
[25] cachem_1.1.0 GenomicAlignments_1.42.0
[27] igraph_2.1.1 lifecycle_1.0.4
[29] iterators_1.0.14 pkgconfig_2.0.3
[31] Matrix_1.7-1 R6_2.5.1
[33] fastmap_1.2.0 PMCMRplus_1.9.12
[35] GenomeInfoDbData_1.2.13 MatrixGenerics_1.18.0
[37] BayesFactor_0.9.12-4.7 digest_0.6.37
[39] colorspace_2.1-1 ShortRead_1.64.0
[41] rematch2_2.1.2 patchwork_1.3.0
[43] S4Vectors_0.44.0 ps_1.8.1
[45] rprojroot_2.0.4 prismatic_1.1.2
[47] GenomicRanges_1.58.0 base64url_1.4
[49] hwriter_1.3.2.1 vegan_2.6-8
[51] labeling_0.4.3 fansi_1.0.6
[53] httr_1.4.7 abind_1.4-8
[55] mgcv_1.9-1 compiler_4.4.2
[57] here_1.0.1 withr_3.0.2
[59] backports_1.5.0 BiocParallel_1.40.0
[61] performance_0.12.4 ggsignif_0.6.4
[63] MASS_7.3-61 DelayedArray_0.32.0
[65] biomformat_1.34.0 permute_0.9-7
[67] tools_4.4.2 ape_5.8
[69] statsExpressions_1.6.1 glue_1.8.0
[71] callr_3.7.6 nlme_3.1-166
[73] rhdf5filters_1.18.0 grid_4.4.2
[75] cluster_2.1.6 reshape2_1.4.4
[77] ade4_1.7-22 generics_0.1.3
[79] gtable_0.3.6 tidyr_1.3.1
[81] data.table_1.16.2 utf8_1.2.4
[83] XVector_0.46.0 BiocGenerics_0.52.0
[85] ggrepel_0.9.6 foreach_1.5.2
[87] pillar_1.9.0 stringr_1.5.1
[89] splines_4.4.2 lattice_0.22-6
[91] gmp_0.7-5 renv_1.0.11
[93] survival_3.7-0 deldir_2.0-4
[95] ggstatsplot_0.12.5 tidyselect_1.2.1
[97] pbapply_1.7-2 Biostrings_2.74.0
[99] IRanges_2.40.0 SummarizedExperiment_1.36.0
[101] stats4_4.4.2 xfun_0.49
[103] Biobase_2.66.0 matrixStats_1.4.1
[105] stringi_1.8.4 UCSC.utils_1.2.0
[107] yaml_2.3.10 kSamples_1.2-10
[109] evaluate_1.0.1 codetools_0.2-20
[111] interp_1.1-6 tibble_3.2.1
[113] BiocManager_1.30.25 multcompView_0.1-10
[115] cli_3.6.3 RcppParallel_5.1.9
[117] secretbase_1.0.3 parameters_0.23.0
[119] munsell_0.5.1 processx_3.8.4
[121] GenomeInfoDb_1.42.0 zeallot_0.1.0
[123] coda_0.19-4.1 png_0.1-8
[125] parallel_4.4.2 rstantools_2.4.0
[127] MatrixModels_0.5-3 bayestestR_0.15.0
[129] latticeExtra_0.6-30 jpeg_0.1-10
[131] bitops_1.0-9 Rmpfr_1.0-0
[133] pwalign_1.2.0 mvtnorm_1.3-2
[135] scales_1.3.0 insight_0.20.5
[137] crayon_1.5.3 rlang_1.1.4 Citation
BibTeX citation:
@online{taudière2024,
author = {Taudière, Adrien},
title = {Alpha-Diversity},
date = {2024-12-03},
langid = {en}
}
For attribution, please cite this work as:
Taudière, Adrien. 2024. “Alpha-Diversity.” December 3,
2024.